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M.Res. Characterising the interactions between major nematode pathogens and the host coffee plant.

  • Full or part time
  • Application Deadline
    Saturday, April 01, 2017
  • Funded PhD Project (UK Students Only)
    Funded PhD Project (UK Students Only)

Project Description

The M.Res (1 year) is funded by Nestle. The project will be jointly supervised by Dr. James McCarthy from Nestle.

Nematode parasitism has adverse effects on coffee plants and subsequent bean production. Current work in the laboratory has established a PCR-based protocol that identifies the economically important root-knot (Meloidogyne spp.) and lesion (Pratylenchus spp.) nematode species from soil samples. Application of those protocols to samples collected from Brazil has shown that diverse species-complexes exist within coffee plantations and also the possibility of inter-species competition on a plant between the different nematodes. Drought is another key constraint to coffee production and drought tolerance is becoming an increasingly important trait for, particularly as climate change leads to drier conditions in some growing regions. As shown for other crop-nematode interactions, the root traits associated with drought tolerance may increase the level of nematode infection that can be supported. It is therefore important that any new coffee cultivars developed for drought tolerance are also evaluated for susceptibility to nematodes.

Overall Aims. The student will help to develop the PCR diagnostic method for improved quantification of nematode species and investigate whether or not there is competition between Meloidogyne and Pratylenchus on coffee plants.
Work Programme. The project will encompass two main Objectives that together will enhance our understanding of the nematode problems in coffee plantations and provide tools with which to address their detection and management. The experimental work will be carried out over approximately nine months, allowing two-three months for completion of all data analysis and thesis preparation.

Objective 1
Develop and improve the PCR diagnostic technique to allow quantification of nematode species from soil samples. The student will carry out PCR diagnostic analysis of field samples collected from coffee plantations to determine the presence of a range of Meloidogyne and Pratylenchus species according to our established protocols. Cost-effectiveness will be improved whilst maintaining robustness and sensitivity of the assay. The analysis will be extended by exploring Droplet Digital (dd)PCR to provide a quantitative assay.

Objective 2
Investigate competition between Meloidogyne and Pratylenchus on coffee plants. Previous fieldwork in Brazil suggested that trees showing damage were more likely to be infected with Meloidogyne whilst Pratylenchus infection was more common in nearby, healthier trees. One possible explanation is that Meloidogyne outcompetes and excludes Pratylenchus. Evidence in the literature also reports competition between the two genera, the effect of which depends on the host plant.
The student will investigate if there is any correlation between the number of Meloidogyne and the presence and/or number of Pratylenchus, and vice versa. They will also determine if the effects of competition are influenced by different coffee cultivars. This data can then be used alongside diagnostic data to characterise the likely impact of the different species complexes in the field.
Plants will be either i) infected simultaneously with equal numbers of Meloidogyne and Pratylenchus nematodes, ii) infected with the two nematode species sequentially, or iii) infected simultaneously with differing proportions of Meloidogyne and Pratylenchus. Single species infections will act as controls.
In each case, roots will be stained after 21 days and analysed for percentage penetration and development of nematodes. Multiplication of each species will be determined at a later time point by extraction of eggs (Meloidogyne) or nematodes (Pratylenchus) from infected roots. If there is evidence of competition then similar experiments will be conducted using plants for which each half of the root system is separated and infected with different nematode species. This would determine if the response is systemic.

The student will spend a period of time visiting Nestle at their research site in Tours, France, accompanying a PhD student from the group who is working on an associated project. The trip will last between 3 and 8 weeks, during which time the student will investigate the potential of ddPCR to provide a quantitative diagnostic nematode assay and will additionally gain experience of working in an industrial setting.

Funding Notes

The M.Res is funded by Nestle.
(i) The full cost of University fees applicable to a UK applicant will be funded.
(ii) Nestle will provide a contribution towards student living expenses of £600 per month – total £7200. Any living expenses beyond that amount will need to be met by the applicant.
(iii) Nestle will also provide support for laboratory consumables.
(iv) Nestle will pay traveling expenses and housing costs for the visit to France.

References

IMPORTANCE OF MELOIDOGYNE AND PRATYLENCHUS SPECIES:
Jones, J. T., Haegeman, A., Danchin, E. G. J., Gaur, H. S., Helder, J., Jones, M. G. K., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M. L., Perry, R. N., (2013). Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology, 14: 946–961.

INFORMATION ON COFFEE PRODUCTION:
International Coffee Organisation (2015). http://www.ico.org/new_historical.asp

COFFEE NEMATODES (MAJORITY OF THE BOOK IS AVAILABLE ONLINE):
Souza, R. M. (2008). Plant-parasitic nematodes of coffee. 1st ed. Dordrecht: Springer.

NEMATODES AND VIETNAM:
Trinh, P. Q., de la Pena, E., Nguyen, C. N., Nguyen, H. X., Moens, M., (2009). Plant-parasitic nematodes associated with coffee in Vietnam. Russian Journal of Nematology, 17(1): 73-82.

NEMATODES AND BRAZIL:
Barros, A. F., OIiveira, R. D. L., Lima, I. M., Coutinho, R. R., Ferreira, A. O., Costa, A., (2014). Root-knot nematodes, a growing problem for Conilon coffee in Espirito Santa state, Brazil. Crop Protection, 55:74-79.

Machado, A. C. Z., (2014). Current nematode threats to Brazilian agriculture. Current Agricultural Science and Technology, 20: 26-35.

DIAGNOSTIC METHODS FOR MELOIDOGYNE IDENTIFICATION:
Adam, M. A. M., Phillips, M. S., Blok, V. C., (2007). Molecular diagnostic key for identification of single juveniles of seven common and economically important species of root-knot nematode (Meloidogyne spp.). Plant Pathology, 56: 190–197.

Randig, O., Bongiovanni, M., Carneiro, R. M. D. G., Castagnone-Sereno, P., (2002), Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species. Genome, 45(5): 862-870

QUANTITATIVE DETECTION METHOD:
Berry, S. D., Fargette, M., Spaull, V. W., Morand, S., Cadet, P., (2008). Detection and quantification of root-knot nematode (Meloidogyne javanica), lesion nematode (Pratylenchus zeae) and dagger nematode (Xiphinema elongatum) parasites of sugarcane using real-time PCR. Mol. Cell. Probes, 22:168–76

MELOIDOGYNE AND PRATYLENCHUS COMPETITION:
BieYun, T. (2008). Competition between Pratylenchus coffeae and Meloidogyne incognita. Plant Pathology Bulletin, 17(4): 271-278.

How good is research at University of Leeds in Biological Sciences?

FTE Category A staff submitted: 60.90

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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